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Starch, as one of the main components in whole-wheat flour (WWF), has a significant impact on the quality of whole grain products. In our previous studies, the reduction of WWF particle sizes by superfine grinding has been shown to enhance the quality of whole-wheat dough and its noodle products. However, the changes in the structures and pasting characteristics of starch in WWF remain unclear when subjected to superfine grinding. The objective of the study is to investigate the influences of superfine grinding on the microstructural, crystalline, molecular structures and pasting characteristics of starch in order to build a correlation between starch structures and its functionality in WWF. Five ranges of particle size distribution of WWF (median diameter: 107, 86, 62, 41, and 21µm) were obtained by superfine grinding. The surface roughness and breakage degree of starch granules were increased with the enhancement of grinding strength. There was a reduction in the intensities of A-type crystalline peaks on the X-ray diffraction patterns due to the alterations of starch crystallites. Small-angle X-ray scattering analysis indicated the disorganization in the semi-crystalline lamellae of starch with thinner lamellae thickness and decreased ordering degree. Additionally, the 13C CP/MAS Nuclear Magnetic Resonance spectra verified the alterations of starch structure by the altered peak shapes of starch carbons (C2, C3, and C5). Along with the structural changes, the pasting properties of starch showed substantial variations, demonstrating increased pasting viscosities and reduced pasting stability. The results suggest that the structures and pasting properties of starch were influenced by superfine grinding although in a non-separated state, the variations of structure and pasting properties could be combined to fully understand the changes of starch functionality in WWF.